Mercurial > repos > iuc > quast
diff quast.xml @ 3:6fcbee531de6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit cd130fcce3254cddb9a3f501f43feaa3f37c1b67
author | iuc |
---|---|
date | Fri, 29 Sep 2017 05:51:26 -0400 |
parents | 2f581f956e1c |
children | 0834c823d4b9 |
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--- a/quast.xml Fri Nov 04 05:06:15 2016 -0400 +++ b/quast.xml Fri Sep 29 05:51:26 2017 -0400 @@ -1,7 +1,7 @@ -<tool id="quast" name="Quast" version="4.1.1" > +<tool id="quast" name="Quast" version="4.5" > <description>Genome assembly Quality</description> <requirements> - <requirement type="package" version="4.1">quast</requirement> + <requirement type="package" version="4.5">quast</requirement> </requirements> <stdio> <regex match="ERROR! exception caught!" @@ -13,6 +13,7 @@ <![CDATA[ #import re quast + --threads \${GALAXY_SLOTS:-4} -o outputdir #if $gene_selection == "eukaryote": --eukaryote @@ -34,7 +35,7 @@ --min-contig $min_contig -l #set names = ','.join( ['"'+ re.sub('[^\w\-_]', '_', str( $x.input.element_identifier))+'"' for $x in $files ]) - + $names --contig-thresholds $threshold_contig #for $k in $files: @@ -48,7 +49,7 @@ mv outputdir/report.tsv '$quast_tsv' && mv outputdir/report.tex '$quast_tex' && mv outputdir/icarus_viewers/contig_size_viewer.html '$icarus' && - mv outputdir/report.html '$report_html' + mv outputdir/report.html '$report_html' ]]> </command> <inputs> @@ -91,6 +92,21 @@ <param name="gene_selection" value="prokaryotes"/> <output name="quast_tsv" file="Quast_report.tsv" lines_diff="4"/> </test> + <test> + <param name="input" value="contigs_1.fasta"/> + <param name="input.type_file" value="contig"/> + <param name="input_ref" value="NC000913.3_1-6650.fasta"/> + <param name="gene_selection" value="prokaryotes"/> + <output name="quast_tsv" file="Quast_report_withref.tsv" lines_diff="4"/> + </test> + <test> + <param name="input" value="contigs_1.fasta"/> + <param name="input.type_file" value="contig"/> + <param name="input_ref" value="NC000913.3_1-6650.fasta"/> + <param name="annot" value="NC000913.3_1-6650.gff"/> + <param name="gene_selection" value="prokaryotes"/> + <output name="quast_tsv" file="Quast_report_withref_withgenes.tsv" lines_diff="4"/> + </test> </tests> <help> <![CDATA[